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comparison 0.2.0/lib/help/polypolish.nf @ 11:a5f31c44f8c9

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author kkonganti
date Mon, 15 Jul 2024 16:11:44 -0400
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10:ddf7a172bf30 11:a5f31c44f8c9
1 // Help text for `polypolish within CPIPES.
2
3 def polypolishHelp(params) {
4
5 Map tool = [:]
6 Map toolspecs = [:]
7 tool.text = [:]
8 tool.helpparams = [:]
9
10 toolspecs = [
11 'polypolish_run': [
12 clihelp: 'Run polypolish tool. Default: ' +
13 (params.polypolish_run ?: false),
14 cliflag: null,
15 clivalue: null
16 ],
17 'polypolish_d': [
18 clihelp: 'A base must occur at least this many times in the pileup to be considered valid. ' +
19 "Default: ${params.polypolish_d}",
20 cliflag: '-d',
21 clivalue: (params.polypolish_d ?: '')
22 ],
23 'polypolish_i': [
24 clihelp: 'A base must make up less than this fraction of the read depth to be considered invalid. ' +
25 "Default: ${params.polypolish_i}",
26 cliflag: '-i',
27 clivalue: (params.polypolish_i ?: '')
28 ],
29 'polypolish_m': [
30 clihelp: 'Ignore alignments with more than this many mismatches and indels. ' +
31 "Default: ${params.polypolish_m}",
32 cliflag: '-m',
33 clivalue: (params.polypolish_m ?: '')
34 ],
35 'polypolish_v': [
36 clihelp: 'A base must make up at least this fraction of the read depth to be considered valid. ' +
37 "Default: ${params.polypolish_v}",
38 cliflag: '-v',
39 clivalue: (params.polypolish_v ?: '')
40 ]
41 ]
42
43 toolspecs.each {
44 k, v -> tool.text['--' + k] = "${v.clihelp}"
45 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
46 }
47
48 return tool
49 }